1. Protein-a chemical view A chain of amino acids folded in 3D Picture from on-line biology bookon-line biology book Peptide Protein backbone N / C terminal

2. Amino Acids 20 types in nature Different properties – side chain Positively charged – Arg, His, Lys A good reference site http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCELL2.htmlA good reference site Negatively charged – Asp, Glu Polar but uncharged – Ser, Thr (OH), Asn, Gln(CO) Special – Cys, Gly, Pro Hydrophobic – Ala, IIe, Leu, Met, Phe, Trp, Tyr, Val, Generally:

3. Protein – a 3D view Bond length, bond angle – fairly restricted Torsion angles on backbone –  (phi),  (psi),  (omega) Picture from http://www.expasy.org/swissmod/course/text/chapter1.htmhttp://www.expasy.org/swissmod/course/text/chapter1.htm , mostly plane(180°, rare case 10°in cis) , , free but with an average characteristic distribution- Ramachandran plot

4. Torsion Angles Dihedral angles  (phi),  (psi),  (omega) N C N C 

5. Secondary structures Helix - hydrogen bond (CO) i -(NH) i+4  -helix (3.6 13 ) 1.5 Å / residue  -sheet is composed of multiple  -strands Picture from www.expasy.org site http://www.expasy.org/swissmod/course/text/chapter1.htm Zig-zag backbone, side-chains opposite directions, ~30°/residue twist, mostly antiparallel Hydrogen bond between two  -strands Turn, loop/coil

6. Protein tertiary and quaternary structure Tertiary – 3D folding of a polypeptide chain involves non-local interaction Quaternary – multiple chains/multi subunits PDB: http://www.pdb.org SCOP database – protein classification

7. Super Secondary Structures  -hairpin 1, 2, 3, 4 residue hairpin,  -meander  -corner http://swissmodel.expasy.org/course/t ext/chapter2.htm helix-hairpin Helix-loop-helix

8. Super Secondary Structures  -hairpin 1, 2, 3, 4 residue hairpin,  -meander  -corner http://swissmodel.expasy.org/course/t ext/chapter2.htm helix-hairpin Helix-loop-helix

9. Classification of Structures Different classification methods Class, architecture, topology and homology CATH – hierarchy http://www.cathdb.info/latest/index.html

10. Protein Folding Problem A protein folds into a unique 3D structure in physiological condition 3D structure is a key to understand function mechanism Rational drug design 3D structure prediction What is the protein folding problem?

11. Sequence  ?  Structure Globin fold 9 structures, 59 critical positions (31+28) 99% to 16% sequence homology No pattern in the critical residues Hydrophobicity of residue